It absolutely is because there are things that you where you cannot tolerate both oposing viewpoints. There's also things that you do not want to tolerate.
Unless you believe it's not okay to be intolerant of murder.
I hope that helps illustrate how it's not just a rhetorical paradox. It's a conceptual one too. Much of the time, it's not tolerance vs intolerance. It's picking between two flavors of intolerance.